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Synthetic Biology Approaches in Cancer Immunotherapy, Genetic Integrative Biology REVIEW ARTICLE Synthetic biology approaches in cancer immunotherapy, genetic network engineering, Downloaded from https://academic.oup.com/ib/article-abstract/8/4/504/5163774 by Columbia University user on 27 March 2020 Cite this: Integr. Biol., 2016, 8, 504 and genome editing Deboki Chakravarti,* Jang Hwan Cho,† Benjamin H. Weinberg,† Nicole M. Wong† and Wilson W. Wong* Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad Received 24th December 2015, and vital role that the synthetic biology approach has played in applying fundamental biological Accepted 31st March 2016 discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields DOI: 10.1039/c5ib00325c of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when www.rsc.org/ibiology developing systems around living cells. Insight, innovation, integration Investigations into cells and their contents have provided evolving insight into the emergence of complex behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending basic discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. We will highlight the role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples illustrate the strength of synthetic approaches, as well as considerations that must be addressed when developing systems around living cells. Introduction areas: sensors, genetic circuits, and genome controls. Sensors allow engineered cells to detect and respond to a variety of Building basic tools with synthetic biology extracellular and intracellular signals, such as cancer antigens,1,2 Cells regularly perform immense tasks, processing signals light,3 and small molecules.4,5 Since the seminal works of the from many sources to gauge and execute a proper response. synthetic toggle switch6 and oscillator,7 many synthetic genetic Over several decades, our knowledge of the components and circuits have been built to program both prokaryotes and connections that underlie these calculations has expanded in eukaryotes with synthetic, complex decision-making systems many organisms, providing the foundation to engineer novel such as logic gates,8 classifiers,9–11 edge detectors,12 counters,13 behaviors into cells. One of the major aims of synthetic biology feedback controllers,14 and finite state machines.15 These and parallel approaches is to translate these discoveries into works have been complemented by the advancement of genome well-characterized and reproducible components of molecular editing tools that have made rapid genome modification feasible engineering. in many species.16–19 The results from work in all three of these While many such engineering parts have been developed areas have produced tools that can be applied towards both the with synthetic biology, this review will focus on three major understanding and engineering of biology. Interrogating biology using synthetic tools Department of Biomedical Engineering, and Biological Design Center, Boston University, Boston, Ma, USA. E-mail: [email protected] The construction of synthetic molecules and circuits has † Equal contribution. enabled scientists to explore the complex networks underlying 504 | Integr. Biol., 2016, 8, 504--517 This journal is © The Royal Society of Chemistry 2016 Review Article Integrative Biology cellular behavior. These studies often fall into either a ‘‘reverse’’ The principles of synthetic biology have taken shape in these or ‘‘forward’’ engineering approach.20 In the ‘‘reverse’’ engi- areas through examinations on the modularity of biology neering strategy, networks in a cell are perturbed at different (chimeric antigen receptors), the use of iterative, computationally- nodes,21 and the resulting changes in behavior provides insights driven design (synthetic oscillators), and the ability to develop tools into the role of different genes and proteins. The complementary for widespread use (genome editing). These characteristics are not ‘‘forward’’ engineering approach enables scientists to hypothesize mutually exclusive, and themes that describe one of these areas and test different design criteria by programming artificial systems of research may be visible in the others. These works also reflect into a cell.22 For instance, artificial feedback loops were generated the fundamental requirement and challenge of synthetic biology: to study the topology involved in controlling the Bacillus subtilus implementation of an engineered system with an environment that 23 competence network dynamics, and synthetic ‘‘secrete and is both complex and not fully understood. The challenges that have Downloaded from https://academic.oup.com/ib/article-abstract/8/4/504/5163774 by Columbia University user on 27 March 2020 sense’’ circuits were developed to investigate the onset of social arisen in these three areas have highlighted gaps in our knowledge or asocial behaviors in yeast.24 and provided further insight into the relevant parameters for these technologies. These new approaches to biology are accompanied Toward commercial applications of synthetic biology by serious questions regarding their safety and practicality. In In addition to elucidating fundamental design principles, syn- assessing the scientific, economic, and ethical considerations that thetic biology has sought to apply the principles of engineering are part of the synthetic biology process, we can gain a deeper cellular behavior towards major challenges in areas such as health understanding of how to build genetic technologies that are and the environment. In some cases, synthetic biology has even applicable to real world challenges. been able to play a major role in commercial product development. Yeast and bacteria are attractive factories to manufacture chemicals that can be otherwise expensive to produce. These organisms Chimeric antigen receptors grow quickly, can be scaled towards large-scale production, and—most importantly for synthetic biology—are relatively Chimeric receptors to understand T cell signaling easy to engineer.25,26 Yeast have been modified through genetic Our adaptive immune system regularly performs complex calcu- engineering to produce the immediate precursor to the potent lations with tremendous consequences for our health. T cells are antimalarial drug artemisinin, providing more stability to the vital to this system, driving the detection, elimination, and production of a drug that was previously reliant on extraction memory of pathogens through processes that are largely directed from the wormwood plant Artemisia annua and thus subject to by the T cell receptor (TCR). The TCR assesses other cells for plant conditions.27,28 The pharmaceutical company Sanofi has signs of pathogen invasion by analyzing epitopes—short peptide licensed the engineered yeast strain to produce more than 39 sequences excised from proteins in the antigen-presenting tonnes of the drug, which can be used for more than 40 million cell (APC)—positioned on the cell surface by the major histo- treatments. Similar strategies to program synthetic pathways in compatibility (MHC) complex. Activation through the TCR is microbes have been developed to produce opioids in yeast29 MHC-restricted, meaning that the receptor must bind to an and biofuels in microorganisms.30–33 MHC-peptide complex to trigger the T cell. In addition to metabolite production, synthetic approaches In the 1980s, the first chimeric receptor to trigger T cell have been critical in the development of cancer therapeutics activation was developed and expressed39 (Fig. 1A). Connecting and disease diagnostics. The engineering of T cells using the variable regions of an antibody to the variable chains of the synthetic cancer-targeting receptors has been hailed as a break- TCR, these chimeric receptors were able to detect antigens and through in cancer therapy due to its unprecedented efficacy activate the T cell upon target-binding (Fig. 1B). This response against leukemia.34 Genetic Boolean logic circuits have been was dictated by the binding of the variable antibody region to expressed in Escherichia coli to detect glycosuria in urine from the target antigen, indicating that this chimeric receptor- diabetic patients,35 and synthetic circuits have been adopted in mediated T cell activation was not MHC-restricted. The clinical a cell-free and paper-based format for the rapid and low cost potential of this receptor to treat cancer was evident and noted detection of various chemicals and Ebola viral RNA.36 in the paper. However, long before the appearance of promising clinical data,
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